Associative Memory Array Processor for Solving Motif Finding Problem

H.M. Faheem (Egypt)


Associative processing systems, DNA sequence analysis, motif finding, and parallel architectures.


This paper provides a novel parallel architecture built on top of associative memory array processor that can be used to accelerate computationally intensive DNA sequences operations. Motif finding problem is suggested as an example of an n-p complete problem. Bit-parallel architecture is proposed such that a set of parallel comparisons could be performed concurrently. The associative memory array processor itself is considered as a type of single instruction stream, multiple data stream machines. The basic building block of the architecture is a 32-bit processing element, which can perform the load and comparison processes. The architecture is of interest because it considerably reduces the time needed to solve the motif finding problem using Brute-Force algorithm. The architecture is considered a step towards a complete parallel architecture for solving computationally intensive problems of bioinformatics.

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